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Winner’s curse correction and variable thresholding improve performance of polygenic risk modeling based on genome-wide association study summary-level data
Jianxin Shi, Ju-Hyun Park, Jubao Duan, Sonja Berndt, Winton Moy, Kai Yu, Lei Song, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, Jonine D Figueroa, Victoria K Cortessis, Núria Malats, Margaret R Karagas, Paolo Vineis, I-Shou Chang, Dongxin Lin, Baosen Zhou, Adeline Seow, Keitaro Matsuo, Yun-Chul Hong, Neil E. Caporaso, Brian Wolpin, Eric Jacobs, Gloria Petersen, Alison P. Klein, Donghui Li, Harvey Risch, Alan R. Sanders, Li Hsu, Robert E. Schoen, Hermann Brenner, MGS (Molecular Genetics of Schizophrenia) GWAS Consortium, GECCO (The Genetics and Epidemiology of Colorectal Cancer Consortium), The GAME-ON/TRICL (Transdisciplinary Research in Cancer of the Lung) GWAS Consortium, PRACTICAL (PRostate cancer AssoCiation group To Investigate Cancer Associated aLterations) Consortium, PanScan and PanC4 Consortium, The GAMEON/ELLIPSE Consortium, Rachael Stolzenberg-Solomon, Pablo Gejman, Qing Lan, Nathaniel Rothman, Laufey T. Amundadottir, Maria Teresa Landi, Douglas F. Levinson, Stephen J. Chanock, Nilanjan Chatterjee
doi: https://doi.org/10.1101/034082
Jianxin Shi
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Ju-Hyun Park
2Statistics Department, Dongguk University, Seoul, Korea.
Jubao Duan
3Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois 60201, USA.
Sonja Berndt
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Winton Moy
4Dept. of Statistics, Northern Illinois Unviersity, DeKalb, IL, 60115, USA.
Kai Yu
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Lei Song
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
William Wheeler
5Information Management Services, Inc., Rockville, MD, 20852, USA.
Xing Hua
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Debra Silverman
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Montserrat Garcia-Closas
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Chao Agnes Hsiung
6Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan.
Jonine D Figueroa
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
7Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Medical School, Edinburgh, United Kingdom.
Victoria K Cortessis
8Department of Preventive Medicine and Department of Obstetrics and Gynecology, USC Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.
9Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.
Núria Malats
10Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Margaret R Karagas
11Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA.
Paolo Vineis
12Human Genetics Foundation, Turin, Italy.
13MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom.
I-Shou Chang
14National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan.
Dongxin Lin
15Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
16State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
Baosen Zhou
17Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China.
Adeline Seow
18Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
Keitaro Matsuo
19Division of Molecular Medicine, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan.
Yun-Chul Hong
20Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
Neil E. Caporaso
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Brian Wolpin
21Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
22Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA.
Eric Jacobs
23Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA.
Gloria Petersen
24Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA.
Alison P. Klein
25Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
26Department of Epidemiology, the Bloomberg School of Public Health, Baltimore, Maryland, USA.
Donghui Li
27Department of Gastrointestinal Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA.
Harvey Risch
28Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA.
Alan R. Sanders
3Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois 60201, USA.
Li Hsu
29Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Robert E. Schoen
30Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA.
Hermann Brenner
31Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
32Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.
33German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
Rachael Stolzenberg-Solomon
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Pablo Gejman
3Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois 60201, USA.
Qing Lan
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Nathaniel Rothman
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Laufey T. Amundadottir
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Maria Teresa Landi
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Douglas F. Levinson
34Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, USA.
Stephen J. Chanock
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
Nilanjan Chatterjee
1Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Mayland 20892, USA.
35Department of Biostatistics and Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21205, USA.
Article usage
Posted January 10, 2016.
Winner’s curse correction and variable thresholding improve performance of polygenic risk modeling based on genome-wide association study summary-level data
Jianxin Shi, Ju-Hyun Park, Jubao Duan, Sonja Berndt, Winton Moy, Kai Yu, Lei Song, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, Jonine D Figueroa, Victoria K Cortessis, Núria Malats, Margaret R Karagas, Paolo Vineis, I-Shou Chang, Dongxin Lin, Baosen Zhou, Adeline Seow, Keitaro Matsuo, Yun-Chul Hong, Neil E. Caporaso, Brian Wolpin, Eric Jacobs, Gloria Petersen, Alison P. Klein, Donghui Li, Harvey Risch, Alan R. Sanders, Li Hsu, Robert E. Schoen, Hermann Brenner, MGS (Molecular Genetics of Schizophrenia) GWAS Consortium, GECCO (The Genetics and Epidemiology of Colorectal Cancer Consortium), The GAME-ON/TRICL (Transdisciplinary Research in Cancer of the Lung) GWAS Consortium, PRACTICAL (PRostate cancer AssoCiation group To Investigate Cancer Associated aLterations) Consortium, PanScan and PanC4 Consortium, The GAMEON/ELLIPSE Consortium, Rachael Stolzenberg-Solomon, Pablo Gejman, Qing Lan, Nathaniel Rothman, Laufey T. Amundadottir, Maria Teresa Landi, Douglas F. Levinson, Stephen J. Chanock, Nilanjan Chatterjee
bioRxiv 034082; doi: https://doi.org/10.1101/034082
Winner’s curse correction and variable thresholding improve performance of polygenic risk modeling based on genome-wide association study summary-level data
Jianxin Shi, Ju-Hyun Park, Jubao Duan, Sonja Berndt, Winton Moy, Kai Yu, Lei Song, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, Jonine D Figueroa, Victoria K Cortessis, Núria Malats, Margaret R Karagas, Paolo Vineis, I-Shou Chang, Dongxin Lin, Baosen Zhou, Adeline Seow, Keitaro Matsuo, Yun-Chul Hong, Neil E. Caporaso, Brian Wolpin, Eric Jacobs, Gloria Petersen, Alison P. Klein, Donghui Li, Harvey Risch, Alan R. Sanders, Li Hsu, Robert E. Schoen, Hermann Brenner, MGS (Molecular Genetics of Schizophrenia) GWAS Consortium, GECCO (The Genetics and Epidemiology of Colorectal Cancer Consortium), The GAME-ON/TRICL (Transdisciplinary Research in Cancer of the Lung) GWAS Consortium, PRACTICAL (PRostate cancer AssoCiation group To Investigate Cancer Associated aLterations) Consortium, PanScan and PanC4 Consortium, The GAMEON/ELLIPSE Consortium, Rachael Stolzenberg-Solomon, Pablo Gejman, Qing Lan, Nathaniel Rothman, Laufey T. Amundadottir, Maria Teresa Landi, Douglas F. Levinson, Stephen J. Chanock, Nilanjan Chatterjee
bioRxiv 034082; doi: https://doi.org/10.1101/034082
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